Novaes said in a statement on Friday that he had asked Brazilian President Jair Bolsonaro and Economy Minister Paulo Guedes for resignation starting from August "understanding that the company needs renewal to meet future innovations in the bank system".
Rubem Novaes has publicly defended the bank's privatization in recent months, local media reported.
Novaes has been heading Banco do Brasil since 2018, before that he had worked in the National Bank for Economic and Social Development.
He has graduated in economics from the Federal University of Rio de Janeiro and completed a master's and doctorate at the University of Chicago.